Find location of a specific point on a UV texture on the 3D object
I figured out a way, although I am not sure if it's the simplest solution:

In order to locate the inner corner of the marker I need a vertex at that point. Therefore I seperated the marker into two faces and created a UV map like this:



Next, using a script (see related lines below) I select the marker and apply the shrinkwrap modifier (it is important to apply it so that the positions of the mesh/vertices are actually affected).  

Since these markers only consist of now five vertices, it is fairly simple to select the one in the center of the marker and read out its local coordinates. Finally, with the object's world matrix I can calculate the inner corner's global position. 

# make the active object the current marker
bpy.context.scene.objects.active = marker

# apply the shrinkwrap modifier to access the exact marker position
bpy.ops.object.modifier_apply (modifier='Shrinkwrap')

# get the local position of the inner corner of the marker
# (assuming the additional vertex in the center is at index 4)
local_inner_corner_pos = marker.data.vertices[4].co 

# calculate marker position with respect to the global coordinate system  
global_inner_corner_pos = marker.matrix_world * local_inner_corner_pos